Input and runtime details for job 3751556 (precomputed example)

Sequence Parameters

	Query ncRNA (short) in FASTA		[.fa]
	Index first query position		1
	Target RNA (long) in FASTA		[.fa]
	Target NCBI RefSeq ID		NC_000913
	All replicons		yes
	Extract sequences around		start codon
	nt upstream (1-300)		75
	nt downstream (1-300)		75
	Index first target position		-75

Output Parameters

	Number of interactions per RNA pair		1
	Suboptimal interaction overlap		can overlap in query
	Max. interaction length		not provided
	Max. absolute energy of an interaction		0
	Max. delta energy above mfe of an interaction		100
	No lonely base pairs		yes
	No GU at helix ends		yes

Seed Parameters

	Min. number of basepairs in seed		7
	Max. Number of mismatches in seed		0
	Maximal energy		0
	Minimal unpaired probability (per RNA)		0
	Seed position (query)		not provided
	Seed position (target)		not provided
	Ignore seeds with GU base pairs		no
	Ignore seeds with GU ends		yes

Folding Parameters

	Temperature for energy computation		37.0
	Access. query: folding window size		150
	Access. query: max. basepair distance		100
	Access. target: folding window size		150
	Access. target: max. basepair distance		100
	Energy parameter set (Vienna package)		Turner model, 2004

Job ID 3751556 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:09:18 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:12:06 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:12:59 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:14:52 CET 2020
	Job Completed		@ Mon Jan 27 14:15:02 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3751556&toolName=IntaRNA ( 30 days expiry )

Description of the job

CyaR - E. coli

Output [zip]

Downloadable files

	IntaRNA result table:		[csv]
	Target region plot		[png] [pdf]
	Query region plot		[png] [pdf]
	Functional enrichment file		[txt]
	Functional annotation chart		[html] [pdf] [png]

Target region plot

Query region plot

Function

Identified Interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Show rows: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 all

Sort by selecting a column name.

Target	Start(T)	End(T)	Start(seed-T)	End(seed-T)	ED(T)	Query	Start(Q)	End(Q)	Start(seed-Q)	End(seed-Q)	ED(Q)	Energy	E(hybrid)	E_norm	RRI subseqs	RRI details	Seq(T)	Seq(Q)	p-value	fdr	gene	geneID	annotation
b1579	-61	-38	-48	-42	6.33	CyaR	9	32	13	19	1.48	-13.17	-20.98	-1.39491	CAGCGGGCUUGUAAUGGGUUAAGU&ACAUAACCCAUAAAAUGCUAGCUG	((((..((.....((((((((.((&)).)))))))).....))..))))	GGGAAUAUCUGCGGCAGCGGGCUUGUAAUGGGUUAAGUGAUAACAGAUGUCUGGAAAUAUAGGGGCAAAUCCACAGGUGAACUACGCUCCUCUGUUUGUUACGCAAUAAAAACUGGUGUUUUCGACUAUGCAAAACAGUUUCCCUCCUCA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0076736	0.9277422	intQ	946130	pseudogene Qin prophage phage integrase familyPhage or Prophage Related
b0704	-71	-37	-43	-37	4.79	CyaR	1	33	1	7	1.49	-13.16	-19.44	-1.39385	ACAGCAGGGAUAGAUGAUUUGGGUGAAAUUUUAGC&GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGU	(((((.....(((((....(((((....(((((((&)))))))......)))))....)).))))))))	AGCAACAGCAGGGAUAGAUGAUUUGGGUGAAAUUUUAGCUAAGAUGAAACAGAGAACAUCGAGAGGAAUAAGAAAAUGAAAAGAGUUUUGUUCUUUUUGCUGAUGAUAUUUGUUAGUUUUGGUGUUAUAGCUGAUUGCGAAAUACAAGCU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0077225	0.9277422	ybfC	947288	putative secreted protein
b4342	-53	-28	-45	-39	2.01	CyaR	5	28	15	21	1.43	-12.97	-16.41	-1.37373	UAGAAAUGUUGUGGGGUUUUGUUUUU&AAAAACAUAACCCAUAAAAUGCUA	(((.....(((((((....(((((((&)))))))...)))))))....)))	UCUGAAAGGUUUUCUUUCAAAUUAGAAAUGUUGUGGGGUUUUGUUUUUGUAUCUUUUAUCUCUAAGGAGCUUGCUUUGGGUCAAUCAGAAUACAUUUCAUGGGUAAAAUGUACUUCCUGGCUAAGUAACUUUGUGAAUCUUAGAGGGUUG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0087074	0.9277422	yjiT	945056	pseudogene
b2568	40	60	54	60	7.67	CyaR	16	38	16	22	4.49	-12.94	-25.1	-1.37055	CUGGUGACGGGCAUUUUAUGG&CCAUAAAAUGCUAGCUGUACCAG	(((((.(((((((((((((((&)))))))))))...)))))))))	GUCGAGCUGCCGCAGGAAGCGUUCCUCGCCAUUCUGCACGUCGGCAAAGACAACAAAUAACCCUUAGGAGUUGGCAUGGCGAAUAUGUUUGCCCUGAUUCUGGUGAUUGCCACACUGGUGACGGGCAUUUUAUGGUGCGUGGAUAAAUUC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0088729	0.9277422	lepB	947040	leader peptidase (signal peptidase I)
b2742	53	72	66	72	6.49	CyaR	24	44	24	30	4.55	-12.91	-23.95	-1.36737	UGGUUUCGCUAUGGCUGGCA&UGCUAGCUGUACCAGGAACCA	(((((((..(((((((((((&)))))))))))...)))))))	UUUUCCAGUGUUCAGUAGGGUGCCUUGCACGGUAAUUAUGUCACUGGUUAUUAACCAAUUUUUCCUGGGGGAUAAAUGAGCGCGGGAAGCCCAAAAUUCACCGUUCGCCGCAUUGCGGCUUUGUCACUGGUUUCGCUAUGGCUGGCAGGC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0090413	0.9277422	nlpD	947011	activator of AmiC murein hydrolase activity lipoprotein
b2859	-59	-36	-46	-40	6.61	CyaR	9	32	13	19	1.48	-12.89	-20.98	-1.36526	CAGCGGGCUUGUAAUGGGUUAAGU&ACAUAACCCAUAAAAUGCUAGCUG	((((..((.....((((((((.((&)).)))))))).....))..))))	ACGGGAAUAUCUGCGGCAGCGGGCUUGUAAUGGGUUAAGUGAUAACAGAUGUCUGGAAAUAUAGGGGCAAAUCCAAUAAACAAUUGGAAUUUACUUCCAUUGAUCUGUUUACUCAGUGGUUGUCACUUUUAUCGAGAAAGGUUUGCAGAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0091552	0.9277422	ygeO	947325	pseudogene orgA family part of T3SS PAI ETT2 remnant
b3482	42	71	42	48	8.56	CyaR	1	35	29	35	1.49	-12.85	-22.9	-1.36102	GUAUGGCGGUAGCAUUGUUCAGGGUUCAGC&GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUAC	(((((((..(((((((.....((((.((((&)))).........))))....))))))))))))))	CAUUGUGACCACAAGUUUUUCUUCGCUUUUUCGUAUGAAGAUACUGUCAUUAAAAUAAUAGAAAAGGAUUUUACGAUGAGCGGAAAACCGGCGGCGCGUCAGGGUGACAUGACGCAGUAUGGCGGUAGCAUUGUUCAGGGUUCAGCCGGG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0093869	0.9277422	rhsB	947994	Rhs protein with DUF4329 family putative toxin domain putative neighboring cell growth inhibitor
b2957	43	68	53	59	7.84	CyaR	22	43	29	35	4.55	-12.83	-25.22	-1.3589	GGUUUUAGUGGUGCAGCAUUGGCAUU&AAUGCUAGCUGUACCAGGAACC	((((....(((((((((..(((((((&))))))))))))))))..))))	UAAAUUGUUUAACGUCAAAUUUCCCAUACAGAGCUAAGGGAUAAUGCGUAGCGUUCACGUAACUGGAGGAAUGAAAUGGAGUUUUUCAAAAAGACGGCACUUGCCGCACUGGUUAUGGGUUUUAGUGGUGCAGCAUUGGCAUUACCCAAU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0095047	0.9277422	ansB	947454	periplasmic L-asparaginase 2
b2308	-11	19	7	13	12.62	CyaR	2	36	14	20	1.49	-12.74	-26.85	-1.34937	GGACAGGCAGCAUGUUGUAUGGGUUUUCAG&CUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACC	((((((..(((((....(((((((((((((&))))))......)))))))..)))))..)))).))	AGAAAGCCCGCUCCCUUCGGGUAACCGGAGGGAGACAAGAGGCGGUAAUUCACCACACACGACAGGACAGGCAGCAUGUUGUAUGGGUUUUCAGGUGUUAUUUUACAGGGUGCGCUCGUCACGCUGGAGCUGGCUAUCAGCUCUGUAGUG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0100518	0.9277422	hisQ	947235	histidine ABC transporter permease
b1278	-56	-30	-56	-50	7.85	CyaR	10	41	35	41	4.6	-12.73	-25.18	-1.34831	UUCCUGGAACUGGCGUUUUCAGUUAUG&CAUAACCCAUAAAAUGCUAGCUGUACCAGGAA	(((((((..((((((((((..((((((&))))))....)))))))))).....)))))))	GGCACAAAUCUGUCAAUUUUUCCUGGAACUGGCGUUUUCAGUUAUGAUUGUGGGACUUAUCAAAAAGGAGAGGCCAUGCGUUCGAUUGCCAGACGUACCGCAGUGGGAGCUGCACUAUUGCUUGUCAUGCCAGUAGCCGUAUGGAUUUCU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0101143	0.9277422	pgpB	945863	phosphatidylglycerophosphatase B

Rows: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 all

Details of Selected Interaction Download Interaction Details

Target

Query

Energy

Hybridization Energy

Unfolding Energy - Target

Unfolding Energy - Query

Position - Target

Position - Query

Position Seed - Target

Position Seed - Query

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When using IntaRNA please cite :

Martin Mann, Patrick R. Wright, and Rolf Backofen
IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions
Nucleic Acids Research, 2017, 45 (W1), W435–W439.
Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Anke Busch, Andreas S. Richter, and Rolf Backofen
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
Bioinformatics, 2008, 24 (24), 2849-56.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with IntaRNA version 3.1.3 linking Vienna RNA package 2.4.14

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